The Tangled Tree
Page 49
Zinder, Norton D., and Joshua Lederberg. 1952. “Genetic Exchange in Salmonella.” Journal of Bacteriology 64 (5).
Zuckerkandl, Emile, and Linus Pauling. 1965a. “Evolutionary Divergence and Convergence in Proteins.” In Evolving Genes and Proteins: A Symposium.” Edited by Vernon Bryson and Henry J. Vogel. New York: Academic Press.
____. 1965b. “Molecules as Documents of Evolutionary History.” Journal of Theoretical Biology 8 (2).
Index
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Page numbers in italics refer to illustrations.
Academic Press, 123
Acinetobacter, 263
Acinetobacter baumannii, 88
acne, 87
acrylamide, 63, 68
adaptation, 176
adenosine triphosphate (ATP), 116, 131, 148
aerobic bacteria, 116
Africa, 127
Agassiz, Louis, 34
Agrobacterium tumefaciens, 154–55
AIDS, 156, 159, 237, 352
Alexander, Leone, 117
Alexander, Morris, 117
algae, 75–76, 192
chloroplasts of, 118, 119
Alliance for the Prudent Use of Antibiotics (APUA), 237, 238
Allmers, Hermann, 169–70
Alm, Eric J., 325–26, 327
alpha-proteobacteria, 155
Alu, 338
American Academy of Arts and Sciences, 159
American Society for Microbiology, 237
amino acids:
proteins formed by, 38–39, 47, 53, 57, 100, 220, 281, 300
in Reciprocating Ratchet Mechanism, 100
ammonites, 33
amobae, 76, 179
amphibians, 182
Anacystis nidulans, 154
Anderson, Ephraim S., 248–49, 255
animals, 92, 188, 189, 190, 193, 212
HGT in, 255, 257–59, 261–64
Linnaeus’s classification of, 15
Antarctica, 85–86
anthrax, 87
Antibiotic Paradox, The (Levy), 238–39
antibiotic-resistant bacteria, 238, 249, 264, 325
from before antibiotics, 244–45
HGT and, xi, 88, 231–35, 236, 239, 245–46, 247
plasmids and, 238, 245, 249
antibiotics, 88, 216, 222–23
antibodies, 364
antimicrobials, 232
antiserum therapy, 216
Apologetics Press, 305
arbre botanique, 13, 14
archaea, 92, 105, 194–95, 200, 287, 309
cell walls of, 208
concept of “species” in, 251, 381
discovery and identification of, x, xi, xii–xiii, 94–95, 98, 99–102, 194, 327
eocytes’ relation to, 203
German workshop on, 108–10, 209
halophiles classified as, 106
HGT as rampant phenomenon among, 284, 294, 297–98
in humans, 317
importance of, xiv
molecular phylogenetics of, 279
naming of, 209–12
novel lineages, 311
and origin of eukaryotes, 375–76
in popular press, 100–101
resistance to idea of, 101–2, 103
sequencing of, 275–76, 280–81, 282
Woese and Kandler’s paper on, 208, 209–12
Archives Research Center, 81–82
Aristotle, 10–11, 13, 179, 182, 283, 380
aspen trees, 383–84
asthma, 316
At Home in the Universe (Kauffman), 331
Atkin, Isobel, 240–41, 242
atmosphere, 95
Augier, Augustin, xiv, 13, 14, 16
Avery, Oswald, xiii, xvi, 220, 242
background of, 221–22
transformation work of, 222, 223, 224, 284, 344
Avery, Roy, 224
bacillary dysentery, 232
bacilli, 87
Bacillus anthracis, 251–52
Bacillus infernus, 85–86
Bacillus subtilis, 252
bacteria, 68, 73, 92, 105, 179, 192, 195, 200, 212, 231, 287, 308
aggregation of, 87–88
Alm’s sequencing of, 325–26, 327
antibiotic-resistant see antibiotic-resistant bacteria
cladistics and, 249–50
classification of, 48–49, 61–65, 72–73, 74–77, 78–79, 83, 87, 249–50, 251–54
concept of “species” in, 251, 252, 330, 381
considered plants, 73
diversity of, 85
evolution of, 50
films formed by, 88
gene sequences of, 240, 276, 280–81, 293
HGT as rampant phenomenon among, 284, 294, 297–98
horizontal gene transfer among, see horizontal gene transfer (HGT)
in humans, 315, 316–17
and idea of individuality, 330–31, 380, 382–83
lack of nuclei in, 190
lactic acid, 88
as large portion of microbes, 71
lithotrophic, 88
location of, 85–86
molecular phylogenetics of, 279
ribosomes in, 53
shapes of, 48, 86–87, 88
size of, 86–87
small genome of, 252–53
as superorganism, 253–54, 383
taxonomy of, 197
total mass of, 86
transformation of, xiii
transposable elements in, 338
bacterial spores, 58
bacterial taxonomy, 71–72
Bacteroides thetaiotaomicron, 316
Baker, Chet, 368
Baker, Kate S., 244, 246
Balch, Bill, 324
at archaea workshop, 108–10
methanogen growing technique of, 78, 83, 84, 93
molecular papers coauthored by, 93–95, 103
Bapteste, Eric, 304
bdelloids, 257–59
Beagle, HMS, 3–4, 7, 24, 30, 167, 341
Bergey, David Hendricks, 74
Bergey’s Manual of Determinative Bacteriology, 74, 75, 109
Beyond God and Darwin (Woese and Sapp), 346–47
Bible, 10, 13, 24
big tree, 195–97, 198–201, 201, 202, 205, 208, 274, 298, 334
biochemical signaling, 104
biofilms, 88
biogenetic law, 177, 184
bioinformatics, 98, 263, 266–67
“Biology’s Next Revolution” (Goldenfeld and Woese), 330–31, 383
biophysics, 196
Bishop, David, 57, 59, 143–44
blepharitis, 87
blood infections, 87
blue-green algae see cyanobacteria
Blyth, Edward, 345
Bonen, Linda, 64–65, 66, 93, 139–40, 142, 144–45, 147, 150, 160, 288
big tree paper coauthored by, 198
mitochondrial endosymbiosis confirmed by, 147–48, 149
Bonnet, Charles, 11, 12, 182
Borneo, 245
bovine insulin, 51, 57
Bowler, Peter J., 184
Brazil, 232
Brenner, Sydney, 40
ribosome’s function discovered by, 52–53
brewer’s yeast, 256, 275
Brock, Thomas, 86, 104, 321–22
Bronn, Heinrich Georg, 177, 178
Broughton-Alcock, William, 243–44, 246
Brown, James R., 279, 280–81
butterflies, 157
Cable, Ernest, 243–44, 246–47
Cameroon, 127
Canada, 108
cancer, 263–64, 316
caused by retroviruses, 352
experiments on, 367
Cancer Genome Atlas, 263
“Can Genes Jump Between Eukaryotic Species,” 256
carbohydrates, 38, 220
Carl XVI Gustav, King, 343
Carl R. Woese Institute for Genomic Biology, 96, 386
Carl Woese Papers, 81–82, 347
catastrophism, 24
caterpillars, 157
cattle, 232
Cavendish Laboratory, 329
celiac disease, 316
Cell in Development and Heredity, The, 121
cells, origin of, 300
cell-to-cell fusion, 355
cellular slime mold, 383
cell walls, 103–5, 300–301
of archaea, 208
Centers for Disease Control and Prevention, U.S., 246
centrioles, 116, 133–34, 135, 136
Chadwick, James, 329
Chagas disease, 341–42
chaos, 74, 330–31
Chardin, Pierre Teilhard de, 191, 193
Charpentier, Emmanuelle, 364
chemical paleogenetics, 42–43, 44–45, 46, 93, 113, 344
see also molecular phylogenetics
Chicago Tribune, 101
chicken, 232
chimpanzees, 382
China, 232
China, William Edward, 185
chloroform, 68
chloroplasts, 118, 190
coining of term, 127
DNA in, 118–19, 121
Doolittle and Bonen’s work on origins of, 140, 142, 144–45
in endosymbiosis, 116, 119, 121, 144–45, 147, 151, 153, 158, 200, 273, 284, 293
genome of, 152, 293–94
Merezhkowsky’s belief in symbiogenesis of, 126, 127–28, 130, 133, 273
cholera, 87
cholesterol, 104
chromosomes, 219, 220
in nucleus, 119
cilia, 133–34, 135, 257
ciliates, 179
Citizen Kane (film), 365–66
cladistics, 249–50
Clark, Michael, 261, 262
Clemens, Frederic, 187
Clinton, Bill, 159, 161, 343
Clostridium difficile, 316–17
Clostridium perfringens, 68
clown fish, 126
Cohn, Ferdinand Julius, xiv, 109, 249
bacteria classified by, 72–73, 74, 75, 87, 102, 251, 252
Collins, Francis, 266
comparative genome studies, 332, 333
complex dynamic systems, 328–29
complexity theory, 330–31, 384
compound 05865, 245
“Concept of a Bacterium, The” (Stanier and van Niel), 76, 77
congenital defects, 360
conjugation, 226, 227, 228, 229, 230
and drug-resistant bacteria, 231, 234, 235
convergence, 191
by endosymbiosis, 193
Copeland, Herbert F., 185–86, 187–88, 189, 210
coral, 7–8
cows, 93
Coyne, Jerry, 304–5, 307
creationism, creationists, 305, 306, 346
Crick, Francis, xiv, 44, 59, 100, 109, 137, 345
DNA discovered by, 37, 38, 39, 344
and evolution of prokaryotes, 50, 51, 57
measuring genealogical relationships by, 37, 40–41, 197, 220, 306, 344
Nobel received by, 344
on origin and deciphering of genetic code, 39–41, 47, 320, 329
and reading of ribosomal RNA, 54–55
and translation of DNA into proteins, 40–41, 51–52, 53, 54
CRISPR, 359–64
Crohn’s disease, 316
crustaceans, 261
crystal growth, 328
Cunningham, Scott, 149–50
Current Biology, 345
cyanobacteria (blue-green algae), 76, 88, 116, 119, 137–39, 145, 151, 153, 154, 192
cyanophytes, 127
cytochrome c, 51
cytoplasm, 118–19, 127, 142
cytoplasmic inheritance, 119, 120–21
Dairy Science, Department of, 93
Darwin, Charles, 3–6, 77, 91, 117, 123, 132, 158, 167, 169, 253, 259, 291, 312, 381, 384-85
Beagle journey of, 3–4, 7, 24, 30, 167, 341
Die Radiolarien read by, 165–66
first inkling of evolution of, 5–6, 26
on heredity, 219
natural selection formulated by, 27–28, 29, 30–31, 132–33, 172, 174, 176, 181, 202, 303, 383
notebooks of, 3, 5–6, 7, 8, 26, 27, 28, 29, 33, 308, 341
tree of life conception of, 6, 7, 8–9, 8, 25, 32–34, 33, 48, 256, 303, 305, 308, 309
Wallace’s manuscript sent to, 30–31
Woese’s disdain for, 331, 335, 345–48, 366, 370, 373
Darwin, Emma Wedgwood, 169
Darwin, Erasmus (brother), 4, 5
Darwin, Erasmus (grandfather), 5, 181, 346
Darwin, Robert, 4–5
Darwin Conspiracy, The (Davies), 346
Darwinian Threshold, 301, 306, 329, 384
Darwin’s Dangerous Idea (Dennett), 302
Darwin’s Playground, 335
Davies, Roy, 346
Dawkins, Richard, 161, 305, 307, 340
de Bary, Anton, 126
Deepwater Horizon oil spill, 88
Delbrück, Max, 109
delta H, 79–80, 82, 83–84, 89, 93
Dennett, Daniel, 304–5, 307
diabetes, 316
diatoms, 126, 179
Die Radiolarien (Haeckel), 165–66, 172
Dioscorides, 13–14
Discover, 158
DNA, x, 44
alphabet of, 37
in chloroplasts, 118–19, 121
discovery of, 37, 38, 39, 344
and evolution of prokaryotes, 51
HGT and, 261–62, 264
junk, 336–42
Sanger’s sequencing of, 154
sequencing of, 51, 55, 154, 262, 274
structure of, 220–21
and transforming principle, 224–25
as transforming principle of bacteria, xiii
translated into proteins, 38–39, 41, 47–48, 51–52
Woese’s study of, 51–52
DNA fibrils, 119
dogs, 294–95
domains, see kingdoms
Doolittle, Ford, xv–xvi, 143, 144–46, 149, 282-84, 292, 303, 305, 319
at archaea conference, 108
belief in “net of life” of, 280
cyanobacteria work of, 137–39, 145
endosymbiosis work of, 137, 139–40, 142, 144–45, 153, 283–84
on genome sequencing of bacteria, 276, 293
Margulis praised by, 160
paper on importance of HGT coauthored by, 3–7, 289–91, 297
philosophical musings of, xv, 307–8, 311
protein trees constructed by, 281
skeptical of HGT’s role in history of life, 278–79
superorganism idea criticized by, 253
on surplus DNA, 340
tree of life updated by, 284–86, 285
Woese’s aid to, 139–40, 143, 144–46, 288
Woese’s break in friendship with, 287–89
double membrane, 119
Doudna, Jennifer, 364
Drosophila ananassae, 262
Dupré, John, 304
dysentery, 87, 233–34, 243–44, 246
Earthly Paradise, The (Merezhkowsky), 125
ecology, 177
eggs, 114, 119, 151, 260, 261–62, 360
Ehrlich, Paul, 343
18S rRNA, 61, 78, 274, 287
Eisen, Jonathan, 267
electron microscopy, 119, 203
electrophoresis, xv, 43, 56, 61–63, 64, 106, 368–69
Elementary Geology (Hitchcock), 24–25, 34
Eli Lilly, 245
Elysia viridis, 158
emergent properties, 330–31, 384
endogenous retroviruses (ERVs), 352–53, 356
endosymbiosis:
as beyond Darwinian theory, 346
&nbs
p; in big tree paper, 200
centrioles and, 116, 133–34, 135, 136
chloroplasts in, 116, 119, 121, 144–45, 147, 153, 273, 284, 293–94
cilia and, 133–34, 135
composite creatures and, 152
convergence by, 193
and DNA in chloroplasts, 119, 121
Doolittle’s work on, 137, 139–40, 142, 144–45, 153, 283–84
flagella and, 133–34, 135
and invention of sex, 134–35
Margulis’s suggestion of, xiv, 113–14, 115–16, 118, 122, 124, 133, 134–37, 142, 144, 147, 149, 150, 151, 160, 162, 191, 273, 293, 312
Martin’s introduction to and study of, 292–93
mitochondria in, 116, 121, 147–48, 151, 152–54, 158, 160, 200, 273, 284, 293–94, 295, 349, 375
rejection of, 151–53
Ris and Plaut’s proposal of, 119–20, 121
see also symbiogenesis; symbionticism; symbiosis
endosymbiotic gene transfer, 294–96, 298, 303–4
energy storage, 104
England, 232, 258
Enterococcus, 245, 246
eocytes, 203–4
episomes, 234–35, 238
see also plasmids
Erlandson, Axel, 310–11, 384
erosion, 24
ERV-L, 352–53
erythromycin, 244
Escherichia, 252
Escherichia coli, 29, 53, 145, 153, 154, 227–28, 230
drug-resistant, 234, 235, 245
genes transferred to brewer’s yeast from, 256
HGT in, 284
sequencing of, 362
Essay on the Principle of Population, An (Malthus), 27
ethanol, 68
Ethiopia, 232
Ettema, Thijs, 311, 375, 376
Euglena gracilis, 121, 133
eukaryotes, 78, 92, 105, 212
centrioles of, 116, 133–34, 135
cilia of, 133–34, 135
eocytes’ relation to, 203
flagella of, 133–34, 135, 190
genetic isolation of, 253
HGT and, 273, 276, 284, 297–98
Margulis’s tree of, 141, 162, 273
mitosis of, 114, 190
molecular phylogenetics of, 279
origins of, 115–16, 122–23, 312, 374–76
prokaryotes vs., 50–51, 75–76, 77, 115, 139
sequencing of genomes of, 275, 281, 374–76
“Everything That Rises Must Converge” (O’Connor), 191
evolution:
Darwin’s first inkling of, 5–6, 26
discovery of archaea as test of, 91–92
HGT’s implications for, 248, 255, 302–6, 330–31
holistic problems of, 344–45
of humans, 173
speed of, 325
see also Lamarckism; natural selection
evolutionary history:
contingency in, x
transitions in, ix–x
exobiology, 99, 120
extinction:
catastrophism and, 24
Darwin on, 7–8, 33
fats, 104, 220
fatty acids, 104